Hypoxia inducible factors and uses thereof for inducing angiogenesis and improving muscular functions

ABSTRACT

This invention provides HIF-3α nucleic acid and sequences. Also provided are methods for using HIF-3α nucleic acids, proteins, fragments, antibodies, probes, and cells, to characterize HIF-3α, modulate HIF-3α cellular levels, induce angiogenesis, improve muscular function, and treat coronary and cardiac diseases in mammals.

RELATED APPLICATIONS

This application claims priority of U.S. Provisional Applications60/292,630 filed May 23, 2001, and 60/354,529 filed Feb. 8, 2002, thedisclosures of which are incorporated by reference herein in theirentireties.

BACKGROUND OF THE INVENTION

a) Field of the Invention

The present invention is concerned with a human protein called “HIF-3α”that is a Hypoxia Inducible Factor-3α and more particularly to the useof HIF-3α nucleic acids, proteins, fragments, antibodies, probes, andcells, to characterize HIF-3α, and modulate its cellular levels.

The present invention is also concerned with the use of nucleotidesequences encoding for proteins from the hypoxia inducible factorsfamily for inducing VEGF expression, for inducing angiogenesis and forimproving muscular functions, and more particularly, for treatingcoronary and cardiac diseases in mammals.

b) Brief Description of the Prior Art

Chronic ischemic heart disease is a worldwide health problem of majorproportions. According to the American Heart Association, 61 800 000Americans have at least one type of cardiovascular disease. Inparticular, coronary heart disease (CHD) cause myocardial infarction(MI) for 7 500 000 American patients and congestive heart failure (CHF)for 4 800 000 American patients. Almost 450 000 deaths in the UnitedStates alone were deemed to derive from CHD.

Current CHD treatments include medication, percutaneous transluminalcoronary angioplasty and coronary artery bypass surgery. Theseprocedures are quite successful to increase blood flow in the myocardiumthus reducing ischemia and ameliorating the condition of the patient.However, due to the progressive nature of CHD, the beneficial effects ofthese procedures are not permanent and new obstructions can occur.Patients that live longer through effective cardiovascular interventionseventually run out of treatment options. Also an important patientpopulation is still refractory to these treatments due to diffuseathereosclerotic diseases and/or small caliber arteries.

Severe and chronic ischemia can cause MI which is an irreversiblescarring of the myocardium. This scarring reduces heart contractilityand elasticity and consequently the pumping function, which can thenlead to CHF. Treatments available to CHF patients target kidney functionand peripheral vasculature to reduce the symptoms but none are treatingthe scar or increasing pump function of the heart. A very promisingapproach for reducing the scar and improving heart function is namedcellular cardiomyoplasty (CCM). It consists in the injection of cells inthe scar, replacing the fibrotic scar by healthy tissue and increasingelasticity (see U.S. Pat. Nos. 5,130,141; 5,602,301, 6,099,832 and6,110,459).

Another emerging treatment for CHF patients is therapeutic angiogenesis.Angiogenesis is defined as blood vessel sprouting and proliferation frompre-existing vasculature. The net result is a higher capillary densityand better blood perfusion. For instance, U.S. Pat. No. 5,792,453disclose a method for promoting coronary collateral vessel developmentby delivering an adenovirus vector with a transgene encoding for anangiogenic protein. Although stimulation of angiogenesis can improvefunction of ischemic myocardium, it will have no effect on scar tissuebecause no viable cells will benefit from the improved perfusion.

Many growth factors are currently used to induce angiogenesis, includingVascular Endothelial Growth Factor (VEGF) and Fibroblast Growth Factor(FGF), but none of these factors has the property to stimulate everystep of angiogenesis (basal membrane disruption, endothelial cellproliferation, migration and differentiation followed by periendothelialcells recruitment). Since it is known that cell hypoxia can naturallyinduce a strong angiogenesis, the use of regulators of hypoxia couldstimulate the synthesis of one or many angiogenic factors at once,thereby resulting in a more structured and stronger angiogenesis thanwith individual factors.

Hypoxia Inducible Factors (HIFs) are heterodimeric transcription factorsthat regulate a number of adaptive responses to low oxygen tension. Theyare composed of alpha- and beta-subunits that belong to the basichelix-loop-helix-PAS (bHLH-PAS) superfamily. Members of this familyinclude HIF-1α (also known as MOP1; see Wang et al., Proc. Natl. Aca.Sci. USA (1995) 92:5510-5514; and U.S. Pat. Nos. 5,882,314; 6,020,462and 6,124,131), HIF-2α (also known as Endothelial PAS 1 (EPAS1), MOP2,HIF-related factor (HRF) and HLF (HIF-like factor), see Tian et al.,Genes & Dev. (1996) 11:72-82; and U.S. Pat. No. 5,695,963).

Another member of the HIF family has been discovered recently, namelyHIF-3α. The cloning of HIF-3α has been described in mice (Gu et al.,Gene Expression (1998) 7:205-213; and in International PCT applicationWO 99/28264) and in rat (Kietzmann et al., Biochem J. (2001), 354(Pt3):531-537). A partial cDNA sequence of human HIF-3α has beenpublished in 1999 (GenBank™ accession No. AF079154), and a full lengthsequence of a human HIF-3α isoform, different from the one of thepresent invention, was published in October 2001 by Hara et al.(Biochem. Biophys. Res. Comm. (2001), Oct. 5; 287:808-813).

HIFs are highly labile in normal conditions, but are stabilized inresponse to low oxygen tension. This stabilization allows them to bindto cis DNA elements of target genes, and stimulate transcription ofhypoxia induced genes that help cell survival in low oxygen conditions.These target genes are implicated in processes such as anaerobicmetabolism (glucose transporters and glycolytic enzymes), vasodilatation(inducible nitric oxide synthase (iNOS) and heme oxygenase-1 (HO-1)),increased breathing (tyrosine hydroxylase), erythropoiesis(erythropoietin) and angiogenesis (VEGF). Gene activation by HIF-1α orHIF-2α was demonstrated by co-transfection assays, in which a reportergene is activated by the co-transfected HIF factor (Tian et al., Genes &Dev. (1996) 11: 72-82; Jiang et al., J. Biol. Chem. (1995) 272:19253-19260). The role of HIF-2α in VEGF activation was alsodemonstrated in renal cell carcinoma (Xia et al., Cancer (2001),91:1429-1436). In animal models, strong angiogenesis was reportedfollowing gene transfer of a hybrid HIF-1α/VP16 DNA construct (Vincentet al., Circulation (2000) 102: 2255-2261). However, prior to thepresent invention, it has never been demonstrated or suggested thatHIF-2α or HIF-3α could induce the expression of angiogenesis-relatedgene(s) in mammalian muscular cells, nor that they could induceangiogenesis in these cells. It was also unknown that expression ofHIF-1α, HIF-2α or HIF-3α in ischemic muscular tissue resulted in anincreased metabolic activity of this tissue, indicating improvedfunction.

Given that HIFs seem to represent ideal factors for VEGF activationand/or for induce angiogenesis, there is thus a need to identify a novelmember of the HIF family. There is more particularly a need for a humanHIF-3α protein and a nucleic acid encoding the same.

Also, it would be highly desirable to be provided with methods,compositions and cells for inducing angiogenesis and for improvingmuscular functions.

The present invention fulfils these needs and also other needs as itwill be apparent to those skilled in the art upon reading the followingspecification.

SUMMARY OF THE INVENTION

The present inventors have discovered a novel member of the humanHypoxia Inducible Factors (HIFs) HIF-3α. The present inventors have alsodiscovered uses for human HIF-3α proteins, fragments, nucleic acids, andantibodies for modulating HIF-3α cellular levels, for inducing VEGFexpression in a mammalian cell, and for inducing angiogenesis in amammalian tissue.

In general, the invention features an isolated or purified nucleic acidmolecule, such as genomic, cDNA, antisense, DNA, RNA or a syntheticnucleic acid molecule that encodes or corresponds to a human HIF-3αpolypeptide.

According to a first aspect, the invention features isolated or purifiednucleic acid molecules, polynucleotides, polypeptides, human HIF-3αproteins and fragment thereof. Preferred nucleic acid molecules consistof a cDNA.

In a first embodiment, the isolated or purified nucleic acid moleculeencodes a human protein that has the biological activity of a humanHIF-3α polypeptide.

According to a specific embodiment, the nucleic acid of the inventioncomprises a sequence selected from the group consisting of:

-   a) sequences provided in SEQ ID NO: 1 or 3;-   b) complements of the sequences provided in SEQ ID NO: 1 or 3;-   c) sequences consisting of at least 20 contiguous residues of a    sequence provided in SEQ ID NO: 1 or 3;-   d) sequences that hybridize to a sequence provided in SEQ ID NO: 1    or 3, under moderately or strong stringent conditions;-   e) sequences having at least 75% identity to a sequence of SEQ ID    NO: 1 or 3; and-   f) degenerate variants of a sequence provided in SEQ ID NO: 1 or 3.

More preferably, the nucleic acid molecule of the invention comprises asequence selected from the group consisting of:

-   a) a nucleotide sequence having at least 75%, 80%, 85%, 90%, 95% or    97% nucleotide sequence identity with SEQ ID NO: 1; and-   b) a nucleotide sequence having at least 75%, 80%, 85%, 90%, 95% or    97% nucleotide sequence identity with a nucleic acid encoding an    amino acid sequence of SEQ ID NO:2.

Even more preferably, the nucleic acid molecule comprises a sequencesubstantially the same or having 100% identity with SEQ ID NO: 1 or asequence substantially the same or having 100% identity with nucleicacids encoding an amino acid sequence of SEQ ID NO: 2. Most preferrednucleic acid molecules are those comprising part or all of nucleic acids1423 to 1545 of SEQ ID NO: 1, and/or those comprising part or all ofnucleic acids encoding a polypeptide with amino acids 475 to 515 of SEQID NO: 2.

According to another specific embodiment, the isolated or purifiednucleic acid molecule comprises a sequence encoding a human HIF-3αpolypeptide or degenerate variants thereof, the human HIF-3α polypeptideor degenerate variant comprising part or all of amino acids 475 to 515of SEQ ID NO: 2. Preferably, the purified nucleic acid moleculecomprises part or all of nucleic acids 1423 to 1545 of SEQ ID NO: 1. Inan even more specific aspect, the invention features an isolated orpurified human nucleic acid molecule comprising a polynucleotide havingthe SEQ ID NO: 1, or degenerate variants thereof, and encoding a humanHIF-3α polypeptide. Preferably, the nucleic acid is a cDNA and itencodes the amino acid sequence of SEQ ID NO: 2 or a fragment thereof.

In a related aspect, the invention features an isolated or purifiednucleic acid molecule which hybridizes under low, preferably moderate,and even more preferably high, stringency conditions to any of thenucleic acid molecules defined hereinbefore. More preferably, suchnucleic acid molecules hybridizes under moderate or high stringencyconditions with part or all of nucleic acids 1423 to 1545 of SEQ ID NO:1, or with part or all of a complementary sequence thereof.

The invention also features substantially pure human polypeptides andproteins that are encoded by any of the above mentioned nucleic acids.In one embodiment, the protein has the biological activity of a humanHIF-3α polypeptide. Preferred biological activity comprises induction ofVEGF expression, thereby promoting angiogenesis.

In another embodiment, the invention aims at an isolated or purifiedpolypeptide comprising an amino acid sequence selected from the groupconsisting of:

-   a) sequences having at least 80% identity to SEQ ID NO: 2;-   b) sequences having at least 85% homology to SEQ ID NO: 2;-   c) sequence provided in SEQ ID NO: 2;-   d) sequences having at least 80% identity to amino acid sequences    encoded by an open reading frame having SEQ ID NO: 3; and-   e) sequences having at least 85% sequence homology to amino acid    sequences encoded by an open reading frame having SEQ ID NO: 3.

More preferably, the polypeptide comprises an amino acid sequenceselected from the group consisting of:

-   a) sequences substantially the same as SEQ ID NO: 2; and-   b) sequences substantially the same as amino acid sequences encoded    by an open reading frame having SEQ ID NO: 3.

In an even more specific aspect, the invention features a substantiallypure human HIF-3α polypeptide or a fragment thereof, comprising part orall of amino acids 475 to 515 of SEQ ID NO: 2, or degenerate variantsthereof. Even more preferably, the polypeptide comprises an amino acidsequence 100% identical to SEQ ID NO: 2.

The present invention also features protein fragments derived from anyof the above mentioned protein or polypeptides. Similarly, the inventionfurther encompasses polypeptides fragment comprising an amino acidsequence encoded by a nucleotide sequence comprising at least 24sequential nucleic acids of SEQ ID NO:1 (hHIF-3α).

The present invention further features an antisense nucleic acid and apharmaceutical composition comprising the same. Preferably, theantisense hybridizes under high stringency conditions to a genomicsequence or to a mRNA so that it reduces human HIF-3α cellular levels ofexpression. According to a first embodiment, the human HIF-3αpolypeptide comprises amino acids 475 to 515 of SEQ ID NO: 2. Morepreferably, the human HIF-3α polypeptide is encoded by an open readingframe having SEQ ID NO: 3. According to a specific embodiment, theantisense hybridizes under high stringency condition with part or all ofSEQ ID NO: 1, or with part or all of a complementary sequence thereof.More preferably, the antisense hybridizes under high stringencyconditions with part or all of nucleic acids 1423 to 1545 of SEQ ID NO:1, with part or all of nucleic acids 2116 to 2223 of SEQ ID NO: 1, orwith part or all of complementary sequences thereof.

The present invention further relates to a pharmaceutical compositioncomprising: (1) at least one element selected from the group consistingof: (i) a nucleic acid molecule encoding a human HIF-3α polypeptide;(ii) a human HIF-3α polypeptide; (iii) an antisense nucleic acid thatreduces a human HIF-3α polypeptide levels of expression; and (iv) anisolated or purified antibody that specifically binds to a HIF-3αpolypeptide; and (2) a pharmaceutically acceptable carrier or diluent.

According to another aspect, the invention features a nucleotide probecomprising a sequence of at least 15, 20, 25, 30, 40, 50, 75 or 100sequential nucleotides of SEQ ID NO: 1 or of a sequence complementary toSEQ ID NO:1. Preferably, the probe comprises part or all of nucleicacids 1423 to 1545 of SEQ ID NO: 1, part or all of nucleic acids 2116 to2223 of SEQ ID NO: 1, part or all of nucleic acids encoding amino acids475 to 515 of SEQ ID NO: 2, or part or all of a complementary sequencethereof. The invention also encompasses a substantially pure nucleicacid that hybridizes under low, preferably moderate, and more preferablyunder high stringency conditions to a probe of at least 20, 25, 30, 40,50, 75 or 100 nucleotides in length that is derived from SEQ ID NO:1.

According to another aspect, the invention features a purified antibody.In a preferred embodiment, the antibody is a monoclonal or a polyclonalantibody that specifically binds to a purified mammalian HIF-3αpolypeptide. Preferably, the antibody specifically binds to a HIF-3αpolypeptide substantially the same as SEQ ID NO:2. More preferably, theantibody specifically binds to a HIF-3α polypeptide comprising part orall of amino acids 475 to 515 of SEQ ID NO: 2 and even more preferably,the antibody specifically binds to part or all of amino acids 475 to 515of SEQ ID NO:2.

In another aspect, the present invention further features a method forinducing VEGF expression in a mammalian cell. The method comprisesintroducing and expressing in the cell a nucleic acid sequence encodingpolypeptide having the biological activity of a human HIF-3αpolypeptide. In a preferred embodiment, the cell consists of a cardiaccell located in the heart of a living mammal, and expression of thepolypeptide induces angiogenesis in cardiac tissue of the mammal. Inanother embodiment, the cell consists of a muscular cell located inmuscular tissue of a living mammal, and expression of the polypeptideinduces angiogenesis in the muscular tissue of the mammal. In anotherembodiment, the mammalian cell is a skeletal muscular cell therebyproviding a HIF-3α expressing-skeletal muscular cell, and the methodfurther comprises the step of transplanting a plurality of the HIF-3αexpressing-skeletal muscular cells in a cardiac tissue of a compatiblemammalian recipient.

Furthermore, the present invention features a method for inducingangiogenesis in a mammalian tissue having a plurality of cells, themethod comprising the step of introducing and expressing in at leastsome of these cells a nucleic acid sequence encoding a polypeptidehaving the biological activity of a human HIF-3α polypeptide.

The present invention also features a method for modulating tumoral cellsurvival or for eliminating a tumoral cell in a mammal, comprising thestep of reducing cellular expression levels of a HIF-3α polypeptide.According to a preferred embodiment, the mammal consists of a human, anda human HIF-3α antisense is introduced into the tumoral cell.

The present invention further features a method for determining theamount of a human HIF-3α polypeptide or a human HIF-3α nucleic acid in abiological sample, comprising the step of contacting the sample with anantibody or with a probe as defined previously.

According to a further aspect, the invention features a method ofevaluating malignancy of a tumor in a human subject, comprising the stepof measuring the amount of a HIF-3α polypeptide or of a HIF-3α nucleicacid in a tumoral cell from the subject, the amount being indicative ofa degree of malignancy for the tumor.

In another related aspect, the invention features a kit for determiningthe amount of a HIF-3α polypeptide in a sample, the kit comprising anantibody or a probe as defined previously, and at least one elementselected from the group consisting of instructions for using the kit,reaction buffer(s), and enzyme(s).

The nucleic acids of the invention may be incorporated into a vector andor a cell (such as a mammalian, yeast, nematode or bacterial cell). Thenucleic acids may also be incorporated into a transgenic animal orembryo thereof. Therefore, the present invention features cloning orexpression vectors, and hosts (such as transformed or transfected cells,transgenic animals) that contain any of the nucleic acids of theinvention and more particularly those encoding a HIF-3α protein,polypeptide or fragment, and those capable of directing expression of aHIF-3α protein, polypeptide or fragment in a vector-containing cell.

In a related aspect, the invention features a method for producing ahuman HIF-3α polypeptide comprising:

-   -   providing a cell transformed with a nucleic acid sequence        encoding a human HIF-3α polypeptide positioned for expression in        this cell;    -   culturing the transformed cell under conditions suitable for        expressing the nucleic acid; and    -   producing the hHIF-3α polypeptide.

One of the greatest advantages of the present invention is that itprovides nucleic acid molecules, proteins, polypeptides, antibodies,probes, and cells that can be used for characterizing HIF-3α, modulateits cellular levels, and promotes angiogenesis.

Other objects and advantages of the present invention will be apparentupon reading the following non-restrictive description of the preferredembodiments thereof and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schema illustrating the human HIF-3α gene organization.

FIG. 2A is a bar graph illustrating the expression of VEGF in HEK293cells transfected with HIF-3α constructs.

FIG. 2B is a bar graph illustrating the expression of VEGF in Hep3Bcells transfected with HIF-3α constructs

FIG. 3A is a bar graph illustrating the expression of VEGF in HEK293cells transfected with HIF-2α constructs.

FIG. 3B is a bar graph illustrating the expression of VEGF in Hep3Bcells transfected with HIF-2α constructs.

FIG. 3C is a bar graph illustrating the expression of VEGF in humanskeletal muscle cells transduced with HIF-2α constructs.

FIG. 4 is a schema showing a possible process of angiogenesis and theprobable role therein of some angiogenesis-related genes.

FIG. 5A is a photograph of HIF-2α modified hSkMC implantedsubcutaneously in mice showing differentiation in myotubes and anorganized vasculature around and in between muscle fiber (arrows pointto vessels).

FIG. 5B is a bar graph that shows the angiogenic activity of HIFconstructs modified hSkMC.

FIG. 6A is a graphic showing the metabolic activity in an ischemic ratheart muscle treated with Ad.HIF-2α.

FIG. 6B is a bar graph that shows the measured blood vessel density inthe infarcted area treated with myocardial HIF-2α gene transfer in rats.

DETAILED DESCRIPTION OF THE INVENTION

A) Definitions

Throughout the text, the word “kilobase” is generally abbreviated as“kb”, the words “deoxyribonucleic acid” as “DNA”, the words “ribonucleicacid” as “RNA”, the words “complementary DNA” as “cDNA”, the words“polymerase chain reaction” as “PCR”, and the words “reversetranscription” as “RT”. Nucleotide sequences are written in the 5′ to 3′orientation unless stated otherwise.

In order to provide an even clearer and more consistent understanding ofthe specification and the claims, including the scope given herein tosuch terms, the following definitions are provided:

Antisense: as used herein in reference to nucleic acids, is meant anucleic acid sequence, regardless of length, that is complementary tothe coding strand of a gene.

Expression: refers to the process by which gene encoded information isconverted into the structures present and operating in the cell. In thecase of cDNAs, cDNA fragments and genomic DNA fragments, the transcribednucleic acid is subsequently translated into a peptide or a protein inorder to carry out its function if any. By “positioned for expression”is meant that the DNA molecule is positioned adjacent to a DNA sequencewhich directs transcription and translation of the sequence (i.e.,facilitates the production of, e.g., a HIF-3α polypeptide, a recombinantprotein or a RNA molecule).

Fragment: Refers to a section of a molecule, such as a protein, apolypeptide or a nucleic acid, and is meant to refer to any portion ofthe amino acid or nucleotide sequence.

Host: A cell, tissue, organ or organism capable of providing cellularcomponents for allowing the expression of an exogenous nucleic acidembedded into a vector or a viral genome, and for allowing theproduction of viral particles encoded by such vector or viral genome.This term is intended to also include hosts which have been modified inorder to accomplish these functions. Bacteria, fungi, animal (cells,tissues, or organisms) and plant (cells, tissues, or organisms) areexamples of a host.

Isolated or Purified or Substantially pure: Means altered “by the handof man” from its natural state, i.e., if it occurs in nature, it hasbeen changed or removed from its original environment, or both. Forexample, a polynucleotide or a protein/peptide naturally present in aliving organism is not “isolated”, the same polynucleotide separatedfrom the coexisting materials of its natural state, obtained by cloning,amplification and/or chemical synthesis is “isolated” as the term isemployed herein. Moreover, a polynucleotide or a protein/peptide that isintroduced into an organism by transformation, genetic manipulation orby any other recombinant method is “isolated” even if it is stillpresent in said organism.

Nucleic acid: Any DNA, RNA sequence or molecule having one nucleotide ormore, including nucleotide sequences encoding a complete gene. The termis intended to encompass all nucleic acids whether occurring naturallyor non-naturally in a particular cell, tissue or organism. This includesDNA and fragments thereof, RNA and fragments thereof, cDNAs andfragments thereof, expressed sequence tags, artificial sequencesincluding randomized artificial sequences.

Open reading frame (“ORF”): The portion of a cDNA that is translatedinto a protein. Typically, an open reading frame starts with aninitiator ATG codon and ends with a termination codon (TAA, TAG or TGA).

Polypeptide: means any chain of more than two amino acids, regardless ofpost-translational modification such as glycosylation orphosphorylation.

Percent identity and Percent similarity: used herein in comparisons ornucleic acid and/or among amino acid sequences. Sequence identity istypically measured using sequence analysis software with the defaultparameters specified therein (e.g., Sequence Analysis Software Packageof the Genetics Computer Group, University of Wisconsin BiotechnologyCenter, 1710 University Avenue, Madison, Owl 53705). This softwareprogram matches similar sequences by assigning degrees of homology tovarious substitutions, deletions, and other modifications. Conservativesubstitutions typically include substitutions within the followinggroups: glycine, alanine, valine, isoleucine, leucine; aspartic acid,glutamic acid, asparagine, glutamine; serine, threonine; lysine,arginine; and phenylalanine, tyrosine.

HIF-3α nucleic acid: means any nucleic acid (see above) encoding amammalian polypeptide that has the biological activity of activating, inan hypoxia inducible fashion, target genes such as VEGF and having atleast 75%, 77%, 80%, 85%, 90%, 95%, 97% or 100% identity or homology tothe amino acid sequence shown in SEQ. ID. NO: 2. Even more preferably,the mammalian HIF-3α polypeptide comprises amino acids having at least75%, 77%, 80%, 85%, 90%, 95%, 97% or 100% identity or homology to aminoacids 475 to 515 of SEQ ID NO: 2. When referring to a human HIF-3αnucleic acid, the nucleic acid encoding SEQ. ID. NO: 2 is moreparticularly concerned. HIF-3α protein or HIF-3α polypeptide: means aprotein, a polypeptide, or a fragment thereof, encoded by a HIF3anucleic acid as described above.

Specifically binds: means an antibody that recognizes and binds aprotein or polypeptide but that does not substantially recognize andbind other molecules in a sample, e.g., a biological sample, thatnaturally includes protein.

Substantially the same: refers to nucleic acid or amino acid sequenceshaving sequence variation that do not materially affect the nature ofthe protein. With particular reference to nucleic acid sequences, theterm “substantially the same” is intended to refer to the coding regionand to conserved sequences governing expression, and refers primarily todegenerate codons encoding the same amino acid, or alternate codonsencoding conservative substitute amino acids in the encoded polypeptide.With reference to amino acid sequences, the term “substantially thesame” refers generally to conservative substitutions and/or variationsin regions of the polypeptide not involved in determination of structureor function of the protein.

Substantially pure polypeptide: means a polypeptide that has beenseparated from the components that naturally accompany it. Typically,the polypeptide is substantially pure when it is at least 60%, byweight, free from the proteins and naturally-occurring organic moleculeswith which it is naturally associated. Preferably, the polypeptide is aHIF-3α polypeptide that is at least 75%, 80%, or 85%, more preferably atleast 90%, 95% or 97% and most preferably at least 99%, by weight, pure.A substantially pure HIF-3α polypeptide may be obtained, for example, byextraction from a natural source (including but not limited to lungcells, kidney cells, heart cells or any other cell expressing HIF-3α) byexpression of a recombinant nucleic acid encoding a HIF-3α polypeptide,or by chemically synthesizing the protein. Purity can be measured by anyappropriate method, e.g., by column chromatography, polyacrylamide gelelectrophoresis, or HPLC analysis. A protein is substantially free ofnaturally associated components when it is separated from thosecontaminants which accompany it in its natural state. Thus, a proteinwhich is chemically synthesized or produced in a cellular systemdifferent from the cell from which it naturally originates will besubstantially free from its naturally associated components.Accordingly, substantially pure polypeptides include those derived fromeukaryotic organisms but synthesized in E. coli or other prokaryotes. By“substantially pure DNA” is meant DNA that is free of the genes which,in the naturally-occurring genome of the organism from which the DNA ofthe invention is derived, flank the gene. The term therefore includes,for example, a recombinant DNA which is incorporated into a vector; intoan autonomously replicating plasmid or virus; or into the genomic DNA ofa prokaryote or eukaryote; or which exists as a separate molecule (e.g.,a cDNA or a genomic or cDNA fragment produced by PCR or restrictionendonuclease digestion) independent of other sequences. It also includesa recombinant DNA which is part of a hybrid gene encoding an additionalpolypeptide sequence.

Transformed or Transfected or Transduced or Transgenic cell: refers to acell into which (or into an ancestor of which) has been introduced, bymeans of recombinant DNA techniques, a DNA molecule encoding (as usedherein) a HIF-3α polypeptide. By “transformation” is meant any methodfor introducing foreign molecules into a cell. Lipofection, calciumphosphate precipitation, retroviral delivery, electroporation, andballistic transformation are just a few of the teachings which may beused.

Transgenic animal: any animal having a cell which includes a DNAsequence which has been inserted by artifice into the cell and becomespart of the genome of the animal which develops from that cell. As usedherein, the transgenic animals are usually mammalian (e.g., rodents suchas rats or mice) and the DNA (transgene) is inserted by artifice intothe nuclear genome.

Vector: A self-replicating RNA or DNA molecule which can be used totransfer an RNA or DNA segment from one organism to another. Vectors areparticularly useful for manipulating genetic constructs and differentvectors may have properties particularly appropriate to expressprotein(s) in a recipient during cloning procedures and may comprisedifferent selectable markers. Bacterial plasmids are commonly usedvectors. Modified viruses such as adenoviruses and retroviruses areother examples of vectors.

B) General Overview of the Invention

The invention generally concerns a protein novel member of the Hypoxiainducible factors (HIFs) HIF-3α. The present inventors have alsodiscovered uses for human HIF-3α proteins, fragments, nucleic acids, andantibodies for modulating HIF-3α cellular levels, for inducing VEGFexpression in a mammalian cell, and for inducing angiogenesis in amammalian tissue. This aspect of the invention also concerns the uses ofhuman HIF-3α proteins, fragments, nucleic acids, and antibodies formodulating HIF-3α cellular levels and for the treatment of coronary andcardiac diseases in mammals, including humans.

The invention also concerns methods and cells, and more particularlygenetically modified muscular cells expressing a plurality ofangiogenesis-related genes, for inducing angiogenesis and for improvingmuscular functions. This additional aspect of the invention is based onthe use of a nucleotide sequence encoding a transcription factor fromthe hypoxia inducible factors family (HIF-1α, HIF-2α, and HIF-3α) andprovides numerous advantages in the treatment of coronary and cardiacdiseases in mammals, including humans.

i) Cloning and Molecular Characterization of HIF-3α

As it will be described hereinafter in the exemplification section ofthe invention, the inventors have discovered, cloned and sequenced ahuman cDNA encoding a new human protein member from the HypoxiaInducible Factor family, called human HIF-3α (hHIF-3α).

The sequence of the HIF-3α cDNA and predicted amino acid sequence isshown in the “Sequence Listing” section. SEQ ID NO: 1 corresponds to thehuman HIF-3α cDNA and SEQ ID NO: 2 corresponds to the predicted aminoacid sequence of the human protein. SEQ ID NO: 3 corresponds to HIF-3αOpen reading frame.

The HIF-3α gene encodes a protein of 705 amino acids (A.A.) long. Insilico analysis indicates that human HIF-3α protein has the followingfeatures: it has a molecular weight of about 76 kDa, an isoelectricpoint of about 5.95; an instability index of about 55.6 (i.e. unstable);an aliphatic index of about 80.6; and a grand average of hydropathicity(GRAVY) of about 0.388. It further comprises many potentialphosphorylation sites (45 Ser, 12 Thr, and 3 Tyr) and also manypotential phosphorylation sites. Predicted protein domains include theHelix Loop Helix (HLH) heterodimerization domain encoded by amino acids14-62. This domain is characteristic of HLH transcription factor family.Then, 2 PAS (A.A. 84-143 and 235-289) and 1 PAC (A.A. 295-337) domainsare identified, these domains are all common to the PAS family (asub-family to the HLH factors).

ii) HIF-3α Homology with Other Genes and Proteins

The cloning of hHIF-3α was carried out starting with the mouse HIF-3αsequence.

A blast search was made to identify sequence identity between hHIF-3α ofthe present invention, mHIF-3α and other existing sequences (see Table 1hereinbelow). It was found that further to mice (GenBank™ accession No.AF060194), HIF-3α had also been sequenced in rat (GenBank™ accession No.NM_(—)022528).

Furthermore, the present inventors also found that their hHIF-3αsequence also shared high level of identity with another, recentlycloned hHIF-3α sequence (GenBank™ accession No. AB054067) published byHara et al. (Biochem. Biophys. Res. Comm. (2001), Oct. 5; 287:808-813).This sequence was published subsequent to the filing date of theapplication on which the present application claims the benefit. TheHara et al. hHIF-3α sequence seems to be another isoform of HIF-3α, thatdiffers from the hHIF-3α according to the present invention since it isdepleted from nucleic acids 1423 to 1545 of SEQ ID NO:1 encoding aminoacids 475 to 515 of SEQ ID NO:2. Equivalent mouse and rat sequences alsolack amino acids homologues to 475-515 amino acids 475 to 515 of SEQ IDNO:2 and are thus homologues of Hara et al. hHIF-3α sequence. Althoughnot shown, nucleic acids 7 to 345 of SEQ ID NO:1 also shares 100%identity with nucleotides 7 to 345 of a partial cDNA sequence of humanHIF-3α published in 1999 (GenBank™ accession No. AF079154), thissequence encoding a 115 amino acid residues (GenBank™ accession No.AAC99397), the last 113 amino acids sharing 100% identity with aminoacids 3 to 115 of SEQ ID NO:2.

TABLE 1 Identified isoform Sequence identity and homology of humanHIF-3α (SEQ ID NOs 1 and 2) to known sequence Amino acid Amino acid GenecDNA identity¹ identity similarity Human HIF-3α² 89% 93% 93% MouseHIF-3α³ 74% 77% 82% Rat HIF-3α⁴ 73% 75% 80% ¹Alignment limited to codingsequence and excluding untranslated regions. ²GenBank access AB054067³GenBank access AF060194 ⁴GenBank access NM_022528

Therefore, the present invention concerns an isolated or purifiednucleic acid molecule (such as cDNA) comprising a sequence selected fromthe group consisting of:

-   a) sequences provided in SEQ ID NO: 1 or 3;-   b) complements of the sequences provided in SEQ ID NO: 1 or 3;-   c) sequences consisting of at least 20 contiguous residues of a    sequence provided in SEQ ID NO: 1 or 3;-   d) sequences that hybridize to a sequence provided in SEQ ID NO: 1    or 3, under moderately or strong stringent conditions;-   e) sequences having at least 75% identity to a sequence of SEQ ID    NO: 1 or 3; and-   f) degenerate variants of a sequence provided in SEQ ID NO: 1 or 3.

More preferably, the nucleic acid molecule of the invention comprises asequence selected from the group consisting of:

-   a) a nucleotide sequence having at least 75%, 80%, 85%, 90%, 95% or    97% nucleotide sequence identity with SEQ ID NO: 1; and-   b) a nucleotide sequence having at least 75%, 80%, 85%, 90%, 95% or    97% nucleotide sequence identity with a nucleic acid encoding an    amino acid sequence of SEQ ID NO:2.

More preferably, the nucleic acid molecule comprises a sequencesubstantially the same or having 100% identity with SEQ ID NO: 1 or asequence substantially the same or having 100% identity with nucleicacids encoding an amino acid sequence of SEQ ID NO: 2. Most preferrednucleic acid molecules are those comprising part or all of nucleic acids1423 to 1545 of SEQ ID NO: 1, and/or those comprising part or all ofnucleic acids encoding a polypeptide with amino acids 475 to 515 of SEQID NO: 2.

The present invention also concerns isolated or purified nucleic acidmolecules comprising a sequence encoding a human HIF-3α polypeptide ordegenerate variants thereof (the human HIF-3α polypeptide or degeneratevariant comprising part or all of amino acids 475 to 515 of SEQ ID NO:2) and purified nucleic acid molecules comprising part or all of nucleicacids 1423 to 1545 of SEQ ID NO: 1.

The present invention also concerns isolated or purified nucleic acidmolecule which hybridizes under moderate, preferably high stringencyconditions with part or all of any of the HIF-3α nucleic acid moleculesof the invention mentioned hereinbefore or with part or all of acomplementary sequence thereof. More preferably, the “hybridizing”nucleic acid hybridizes under moderate, preferably high stringencyconditions with part or all of nucleic acids 1423 to 1545 of SEQ ID NO:1, or with part or all of a complementary sequence thereof. The“hybridizing” nucleic acid could be used as probe or as antisensemolecules as it will be described hereinafter.

In a related aspect, the present invention concerns an isolated orpurified polypeptide, comprising an amino acid sequence selected fromthe group consisting of:

-   a) sequences encoded by part or all of the HIF-3α nucleic acid    molecules of the invention mentioned hereinbefore;-   b) sequences having at least 80% identity to SEQ ID NO: 2;-   c) sequences having at least 85% homology to SEQ ID NO: 2;-   d) sequence provided in SEQ ID NO: 2;-   e) sequences having at least 80% identity to amino acid sequences    encoded by an open reading frame having SEQ ID NO: 3; and-   f) sequences having at least 85% sequence homology to amino acid    sequences encoded by an open reading frame having SEQ ID NO: 3.

More preferably, the polypeptide comprises an amino acid sequencesubstantially the same or having 100% identity with SEQ ID NO: 2 or asequence substantially the same or having 100% identity with amino acidsequences encoded by an open reading frame having SEQ ID NO: 3. Eventmore preferably, the polypeptides comprise part or all of amino acids475 to 515 of SEQ ID NO: 2, or degenerate variants thereof, or comprisepart or all of amino acids encoded by nucleic acids 1423 to 1545 of SEQID NO: 1. Most preferred polypeptides are those having the biologicalactivity of a human HIF-3α polypeptide, such as VEGF expressioninducement capabilities for the promotion of angiogenesis.

iii) Vectors, Cells and Transgenic Animals

The invention is also directed to a host, such as a genetically modifiedcell, expressing a functional HIF-3α transcription factor. Preferably,the cell is a skeletal muscular cell or a cardiac cell. Preferably also,the cell comprises a cDNA encoding the transcription factor.

The HIF-3α expressing cell may be a transiently-transfected mammaliancell line (such as HEK293 cells, a Hep3B cells, and the like) or anysuitable isolated primary cells, including by not limited to mammalianskeletal muscular cells, cardiac cells, bone marrow cells, fibroblasts,smooth muscle cells, endothelial cells, endothelial progenitor cells andembryonic stem cells

A number of vectors suitable for stable transfection of mammalian cellsare available to the public (e.g. plasmids, adenoviruses,adeno-associated viruses, retroviruses, Herpes Simplex Viruses,Alphaviruses, Lentiviruses), as are methods for constructing such celllines. The present invention encompasses any type of vector with aHIF-3α sequence.

The cells of the invention may be particularly useful when transplantedin a compatible recipient for inducing angiogenesis, relieving ischemia,increasing the metabolic activity of a mammalian muscular tissue, and/orincreasing muscular function in CHF or in peripheral vascular disease,locally or in surrounding transplanted tissue. Of course, thegenetically modified cells of the present invention could also be usedfor the formation of artificial organs or for tissue constructions.HIF-3α expressing cells may also be used for producing HIF-3α andderivatives thereof (see hereinafter).

The mammalian HIF-3α according to the present invention or a fragmentthereof may also be used to generate 1) transgenic animals that expressthe HIF-3α gene or HIF-3α mutants at various levels in one or multiplecell lineages, 2) knock-out animal in which expression of the endogenousHIF-3α gene is either prevented or regulated in one or multiple celllineages.

Characterization of HIF-3α genes provides information that is necessaryfor a HIF-3α knockout animal model to be developed by homologousrecombination. Preferably, the model is a mammalian animal, mostpreferably a mouse. Similarly, an animal model of HIF-3α overproductionmay be generated by integrating one or more HIF-3α sequences into thegenome, according to standard transgenic techniques.

iv) Synthesis of HIF-3α and Functional Derivative thereof

Knowledge of human HIF-3α gene sequence open the door to a series ofapplications. For instance, the characteristics of the cloned HIF-3αgene sequence may be analyzed by introducing the sequence into variouscell types or using in vitro extracellular systems. The function ofHIF-3α may then be examined under different physiological conditions.The HIF-3α cDNA sequence may be manipulated in studies to understand theexpression of the gene and gene product. Alternatively, cell lines maybe produced which overexpress the gene product allowing purification ofHIF-3α for biochemical characterization, large-scale production,antibody production, and patient therapy.

For protein expression, eukaryotic and prokaryotic expression systemsmay be generated in which the HIF-3α gene sequence is introduced into aplasmid or other vector which is then introduced into living cells.Constructs in which the HIF-3α cDNA sequence containing the entire openreading frame inserted in the correct orientation into an expressionplasmid may be used for protein expression. Alternatively, portions ofthe sequence, including wild-type or mutant HIF-3α sequences, may beinserted. Prokaryotic and eukaryotic expression systems allow variousimportant functional domains of the protein to be recovered as fusionproteins and then used for binding, structural and functional studiesand also for the generation of appropriate antibodies.

Eukaryotic expression systems permit appropriate post-translationalmodifications to expressed proteins. This allows for studies of theHIF-3α gene and gene product including determination of properexpression and post-translational modifications for biological activity,identifying regulatory elements located in the 5′ region of the HIF-3αgene and their role in tissue regulation of protein expression. It alsopermits the production of large amounts of normal and mutant proteinsfor isolation and purification, to use cells expressing HIF-3α as afunctional assay system for antibodies generated against the protein, totest the effectiveness of pharmacological agents or as a component of asignal transduction system, to study the function of the normal completeprotein, specific portions of the protein, or of naturally occurringpolymorphisms and artificially produced mutated proteins. The HIF-3α DNAsequence may be altered by using procedures such as restriction enzymedigestion, DNA polymerase fill-in, exonuclease deletion, terminaldeoxynucleotide transferase extension, ligation of synthetic or clonedDNA sequences and site directed sequence alteration using specificoligonucleotides together with PCR.

Accordingly, the invention also concerns a method for producing a humana human HIF-3α polypeptide. The method comprises the steps of: (i)providing a cell transformed with a nucleic acid sequence encoding ahuman HIF-3α polypeptide positioned for expression in the cell; (ii)culturing the transformed cell under conditions suitable for expressingthe nucleic acid; (iii) producing said a human HIF-3α polypeptide; andoptionally, (iv) recovering the human HIF-3α polypeptide produced.

Once the recombinant protein is expressed, it is isolated by, forexample, affinity chromatography. In one example, an anti-HIF-3αantibody, which may be produced by the methods described herein, can beattached to a column and used to isolate the HIF-3α protein. Lysis andfractionation of HIF-3α-harboring cells prior to affinity chromatographymay be performed by standard methods. Once isolated, the recombinantprotein can, if desired, be purified further.

Methods and techniques for expressing recombinant proteins and foreignsequences in prokaryotes and eukaryotes are well known in the art andwill not be described in more detail. One can refer, if necessary toJoseph Sambrook, David W. Russell, Joe Sambrook Molecular Cloning: ALaboratory Manual 2001 Cold Spring Harbor Laboratory Press. Thoseskilled in the art of molecular biology will understand that a widevariety of expression systems may be used to produce the recombinantprotein. The precise host cell used is not critical to the invention.The HIF-3α protein may be produced in a prokaryotic host (e.g., E. coil)or in a eukaryotic host (e.g., S. cerevisiae, insect cells such as Sf21cells, or mammalian cells such as COS-1, NIH 3T3, or HeLa cells). Thesecells are publicly available, for example, from the American TypeCulture Collection, Rockville, Md. The method of transduction and thechoice of expression vehicle will depend on the host system selected.

Polypeptides of the invention, particularly short HIF-3α fragments, mayalso be produced by chemical synthesis. These general techniques ofpolypeptide expression and purification can also be used to produce andisolate useful HIF-3α fragments or analogs, as described herein.

Skilled artisans will recognize that a mammalian HIF-3α, or a fragmentthereof (as described herein), may serve as an active ingredient in atherapeutic composition. This composition, depending on the HIF-3α orfragment included, may be used to regulate cell proliferation, survivaland angiogenesis and thereby treat any condition that is caused by adisturbance in cell proliferation, accumulation or replacement. Thus, itwill be understood that another aspect of the invention describedherein, includes the compounds of the invention in a pharmaceuticallyacceptable carrier.

v) Upregulation of HIF-3α Expression for Promoting Angiogenesis

Knowledge of human HIF-3α gene sequence provides novel promisingapproaches for patient therapy. As it will be shown in detailshereinafter in the exemplification section of the application,upregulation of HIF-3α expression could be used to increase VEGFexpression in mammalian cells and thereby promote angiogenesis inischemic and non-ischemic tissue of mammals, preferably animal modelsand humans.

Therefore, the invention also relates to methods for inducing VEGFexpression in a mammalian cell by introducing and expressing in the cella nucleic acid sequence encoding polypeptide having the biologicalactivity of a human HIF-3α polypeptide. Of course, other nucleic acids,such as those which expression is known to also induce VEGF expression,may be introduced and expressed in the cell together with HIF-3α.

Another related aspect of the invention concerns methods for inducingangiogenesis in a mammalian tissue having a plurality of cells, byintroducing and expressing in at least some of these cells a nucleicacid sequence encoding a polypeptide having the biological activity of ahuman HIF-3α polypeptide.

Preferably, these methods are achieved by transfecting in vitro, in vivoor ex vivo cells with a HIF-3α cDNA, the human HIF-3α polypeptidecomprises an amino acid sequence substantially the same as SEQ ID NO:2.

As mentioned previously in the “background” section, stimulation ofangiogenesis may be beneficial for the treatment of coronary heartdiseases. Therefore, the human HIF-3α sequence of the invention could beadvantageously used for such purposes. In one embodiment, the cellconsists of a cardiac cell located in the heart of a living mammal, andthe HIF-3α nucleic acid sequence is introduced in a plurality of thesecardiac cell such that expression of the HIF-3α polypeptide induceangiogenesis in cardiac tissue of the mammal. Introduction of the HIF-3αnucleic acid sequence may be done by using a vector as definedpreviously or by any suitable technique known in the art.

In another embodiment, the cell consists of an isolated muscular cell(preferably skeletal muscular cell), and this cell is geneticallymodified so as to express the HIF-3α polypeptide. Genetically modifiedHIF-3α expressing cells are then transplanted in tissue (e.g. cardiactissue) of a compatible mammalian recipient. More preferably, thetransplantation is autologous (the cells are isolated from musculartissue, such as leg, of the recipient), and the cells are transplantedto the recipient (such as an injection in the scar of the heart) in anamount that is sufficient to induce angiogenesis locally or insurrounding transplanted tissue.

In yet another embodiment, the cell consists of a muscular cell locatedin muscular tissue of a living mammal, and expression of the HIF-3αpolypeptide induce angiogenesis in the muscular tissue of the mammal(autologous or heterologous transplantation). This method isparticularly useful for treating peripheral artery diseases (e.g.ischemia in the legs due to femoral or upstream artery obstruction inhumans).

The nucleotide sequence may be introduced in the cell or tissue usingwell known methods. Indeed, the sequence(s) may be introduced directlyin the cells of a given tissue, injected in the tissue, or introducedvia the transplantation of previously genetically modified compatiblecells (see hereinafter). Methods for introducing a nucleotide sequenceinto eukaryote cells such as mammalian muscular cells or for geneticallymodifying such cells are well known in the art. For instance, this maybe achieved with adenoviral vectors, plasmid DNA transfer (naked DNA orcomplexed with liposomes) or electroporation. If necessary, a personskilled in the art may look at Isner J., (Nature (2002), 415:234-239)for a review of myocardial gene therapy methods and to U.S. patentapplication US20010041679A1 or U.S. Pat. No. 5,792,453 which providesmethods of gene transfer-mediated angiogenesis therapy. Preferably, thelevel of expression of the transcription factor(s) is such that theangiogenesis-related gene is expressed at a level that is sufficient toinduce angiogenesis locally or in surrounding tissue. For bettercontrolling its expression and selectivity, the transcription factor maybe inducible.

In preferred embodiments, a plurality of genetically modified skeletalmuscular cells are transplanted into the heart of a compatiblerecipient. Preferably, the transplantation is autologous. Morepreferably, the cells are transplanted in an amount that is sufficientto induce angiogenesis locally or in surrounding transplanted tissue.Even more preferably, the transplantation improves the recipient'scardiac functions. Transplantation methods, are well known in the art.For detailed examples of muscular cell transplantation, one may refer toU.S. Pat. Nos. 5,602,301 and 6,099,832.

vi) Downregulation of HIF-3α Expression

As mentioned previously, HIF-3α expression induces VEGF expression,which itself promotes angiogenesis. Since it is well known that tumoralcell survival depend on angiogenesis, we propose that, in some tumors,HIF-3α expression is essential for cancer cell proliferation.Accordingly, downmodulation of HIF-3α could be used to prevent and/ortreat these tumors.

Therefore, the invention relates to methods for modulating tumoral cellsurvival or for eliminating a tumoral cell in a human by reducingcellular expression levels of a human HIF-3α polypeptide. In a preferredembodiment, this is achieved by delivering an antisense into the tumoralcells. This can be achieved by intravenous injection, intratumoralinjection or other local drug delivery using currently available methods(e.g. Crooke et al., (2000), Oncogene 19, 6651-6659; Stein et al.(2001), J Clin. Invest 108, 641-644; and Tamm et al., (2001), Lancet358, 489-497).

According to a related aspect of the above-mentioned method, theinvention relates to antisense nucleic acids and to pharmaceuticalcompositions comprising such antisenses, the antisense being capable ofreducing HIF-3α cellular levels of expression, and more particularly thelevel of expression of human HIF-3α polypeptide encoded by an openreading frame having SEQ ID NO: 3 and/or comprising amino acids 475 to515 of SEQ ID NO: 2. Preferably, the antisense nucleic acid iscomplementary to a nucleic acid sequence encoding a hHIF-3α protein orencoding any of the polypeptides derived therefrom. More preferably, theantisense hybridizes under high stringency conditions to a genomicsequence or to a mRNA, even more preferably under high stringencyconditions with part or all of SEQ ID NO: 1, or with part or all of acomplementary sequence thereof. Most preferred antisense molecules arethose which hybridize under high stringency conditions with part or allof nucleic acids 1423 to 1545 of SEQ ID NO: 1, with part or all ofnucleic acids 2116 to 2223 of SEQ ID NO: 1, or with part or all ofcomplementary sequences thereof.

A non-limitative example of high stringency conditions includes:

-   -   a) pre-hybridization and hybridization at 68° C. in a solution        of 5×SSPE (1×SSPE=0.18 M NaCl, 10 mM NaH₂P0₄); 5× Denhardt        solution; 0.05% (w/v) sodium dodecyl sulfate (SDS); et 100 μg/ml        salmon sperm DNA;    -   b) two washings for 10 min at room temperature with 2×SSPE and        0.1% SDS;    -   c) one washing at 60° C. for 15 min with 1×SSPE and 0.1% SDS;        and    -   d) one washing at 60° C. for 15 min with 0.1×SSPE et 0.1% SDS.        vii) HIF-3α Antibodies

The invention features purified antibodies that specifically binds to aHIF-3α protein. The antibodies of the invention may be prepared by avariety of methods using the HIF-3α proteins or polypeptides describedabove. For example, the HIF-3α polypeptide, or antigenic fragmentsthereof, may be administered to an animal in order to induce theproduction of polygonal antibodies. Alternatively, antibodies used asdescribed herein may be monoclonal antibodies, which are prepared usinghybridoma technology (see, e.g., Hammerling et al., In MonoclonalAntibodies and T-Cell Hybridomas, Elsevier, N.Y., 1981). The inventionfeatures antibodies that specifically bind human HIF-3α polypeptides, orfragments thereof. In particular, the invention features “neutralizing”antibodies. By “neutralizing” antibodies is meant antibodies thatinterfere with any of the biological activities of the HIF-3αpolypeptide, particularly the ability of HIF-3α to induce VEGFexpression. The neutralizing antibody may reduce the ability of HIF-3αpolypeptides to inhibit VEGF expression by, preferably 50%, morepreferably by 70%, and most preferably by 90% or more. Any standardassay of VEGF expression, including those described herein, may be usedto assess potentially neutralizing antibodies. Once produced, monoclonaland polyclonal antibodies are preferably tested for specific HIF-3αrecognition by Western blot, immunoprecipitation analysis or any othersuitable method.

In addition to intact monoclonal and polyclonal anti-HIF-3α antibodies,the invention features various genetically engineered antibodies,humanized antibodies, and antibody fragments, including F(ab′)2, Fab′,Fab, Fv and sFv fragments. Antibodies can be humanized by methods knownin the art. Fully human antibodies, such as those expressed intransgenic animals, are also features of the invention.

Antibodies that specifically recognize HIF-3α (or fragments of HIF-3α),such as those described herein, are considered useful to the invention.Such an antibody may be used in any standard immunodetection method forthe detection, quantification, and purification of a HIF-3α polypeptide.Preferably, the antibody binds specifically to HIF-3α. The antibody maybe a monoclonal or a polyclonal antibody and may be modified fordiagnostic or for therapeutic purposes. More preferably the antibodyspecifically binds the a HIF-3α polypeptide comprising part or all ofamino acids 475 to 515 of SEQ ID NO:2. The most preferred antibodies arethose that specifically binds to part or all of amino acids 475 to 515of SEQ ID NO:2.

The antibodies of the invention may, for example, be used in animmunoassay to monitor HIF-3α expression levels, to determine thesubcellular location of a HIF-3α or HIF-3α fragment produced by a mammalor to determine the amount of HIF-3α or fragment thereof in a biologicalsample. Antibodies that inhibit HIF-3α described herein may beespecially useful for conditions where decreased HIF-3α function wouldbe advantageous such as inhibition of cancer cell proliferation (seehereinafter). In addition, the antibodies may be coupled to compoundsfor diagnostic and/or therapeutic uses such as radionucleotides forimaging and therapy and liposomes for the targeting of compounds to aspecific tissue location. The antibodies may also be labeled (e.g.immunofluorescence) for easier detection.

viii) Administration of HIF-3α Polypeptides, Modulators of HIF-3αSynthesis or Function

Therapies may be designed to circumvent or overcome an inadequate HIF-3αgene expression. This could be accomplished for instance by transfectionof HIF-3α cDNA.

To obtain large amounts of pure HIF-3α, cultured cell systems would bepreferred. Delivery of the protein to the affected tissues can then beaccomplished using appropriate packaging or administrating systems.Alternatively, it is conceivable that small molecule analogs could beused and administered to act as HIF-3α agonists and in this mannerproduce a desired physiological effect. Methods for finding suchmolecules are provided herein.

A HIF-3α protein or polypeptide, polypeptide, antibody or modulator(e.g. antisense) may be administered within a pharmaceuticallyacceptable diluent, carrier, or excipient, in unit dosage form.Conventional pharmaceutical practice may be used to provide suitableformulations or compositions to administer HIF-3α protein, polypeptide,or modulator to patients. Administration may begin before the patient issymptomatic. Any appropriate route of administration may be employed,for example, administration may be parenteral, intravenous,intraarterial, subcutaneous, intramuscular, intracranial, intraorbital,ophthalmic, intraventricular, intracapsular, intraspinal,intracisternal, intraperitoneal, intranasal, aerosol, by suppositories,or oral administration. Therapeutic formulations may be in the form ofliquid solutions or suspensions; for oral administration, formulationsmay be in the form of tablets or capsules; and for intranasalformulations, in the form of powders, nasal drops, or aerosols.

Methods well known in the art for making formulations are found, forexample, in “Remington's Pharmaceutical Sciences.” Formulations forparenteral administration may, for example, contain excipients, sterilewater, or saline, polyalkylene glycols such as polyethylene glycol, oilsof vegetable origin, or hydrogenated napthalenes. Biocompatible,biodegradable lactide polymer, lactide/glycolide copolymer, orpolyoxyethylene-polyoxypropylene copolymers may be used to control therelease of the compounds. Other potentially useful parenteral deliverysystems include ethylene-vinyl acetate copolymer particles, osmoticpumps, implantable infusion systems, and liposomes. Formulations forinhalation may contain excipients, for example, lactose, or may beaqueous solutions containing, for example, polyoxyethylene-9-laurylether, glycocholate and deoxycholate, or may be oily solutions foradministration in the form of nasal drops, or as a gel.

If desired, treatment with a HIF-3α protein, polypeptide, or modulatorycompound may be combined with more traditional therapies for the diseasesuch as surgery, steroid therapy, or chemotherapy.

According to a preferred embodiment, a HIF-3α antisense would beincorporated in a pharmaceutical composition comprising at least one ofthe oligonucleotides defined previously, and a pharmaceuticallyacceptable carrier. The amount of antisense present in the compositionof the present invention is a therapeutically effective amount. Atherapeutically effective amount of antisense is that amount necessaryso that the antisense performs its biological function without causingoverly negative effects in the host to which the composition isadministered. The exact amount of oligonucleotides to be used andcomposition to be administered will vary according to factors such asthe oligo biological activity, the type of condition being treated, themode of administration, as well as the other ingredients in thecomposition. Typically, the composition will be composed of about 1% toabout 90% of antisense, and about 20 μg to about 20 mg of antisense willbe administered. For preparing and administering antisenses as well aspharmaceutical compositions comprising the same, methods well known inthe art may be used. For instance, see Crooke et al (Oncogene, 2000,19:6651-6659) and Tamm et al. (Lancet 200,1358:489-497) for a review ofantisense technology in cancer chemotherapy.

ix) Assessment of HIF-3α Intracellular or Extracellular Levels

As noted, the antibodies and probes described above may be used tomonitor HIF-3α protein expression and/or to determine the amount ofHIF-3α or fragment thereof in a biological sample, and/or to evaluatemalignancy of a tumor in a human subject.

In addition, in situ hybridization may be used to detect the expressionof the HIF-3α gene. As it is well known in the art, in situhybridization relies upon the hybridization of a specifically labelednucleic acid probe to the cellular RNA in individual cells or tissues.Therefore, oligonucleotides or cloned nucleotide (RNA or DNA) fragmentscorresponding to unique portions of the HIF-3α gene may be used to assesHIF-3α cellular levels or detect specific mRNA species. Such anassessment may also be done in vitro using well known methods (Northernanalysis, quantitative PCR, etc.).

Determination of the amount of HIF-3α or fragment thereof in abiological sample may be especially useful for diagnosing a cellproliferative disease or an increased likelihood of such a disease,particularly in a human subject, using a HIF-3α nucleic acid probe orHIF-3α antibody. The present inventor also suspect that there exist acorrelation between the degree of malignancy of certain types of tumorwith the amount HIF-3α or fragment thereof, and that high levels ofHIF-3α is indicative that the tumoral cells have a higher angiogenesisactivity and malignancy. Highly malignant cancers are cancers whichcells display a short doubling time (e.g. hematopoietic cancer, lungcancers, prostate cancer, testis cancer, breast cancer, melanomas,pancreatic cancer intestine cancers, sarcomas, prostate cancer andhematologic cancers).

The methods of the invention may be carried out by contacting, in vitroor in vivo, a biological sample (such as a blood sample or a tissuebiopsy) from an individual suspected of harboring cancer cells, with aHIF-3α antibody or a probe according to the invention, in order toevaluate the amount of HIF-3α in the sample or the cells therein. Themeasured amount would be indicative of the probability of the subject ofhaving proliferating tumoral cells since it is expected that these cellshave a higher level of HIF-3α expression.

In a related aspect, the invention features a method for detecting theexpression of HIF-3α in tissues comprising, i) providing a tissue orcellular sample; ii) incubating said sample with an anti-HIF-3αpolyclonal or monoclonal antibody; and iii) visualizing the distributionof HIF-3α.

Assay kits for determining the amount of HIF-3α in a sample would alsobe useful and are within the scope of the present invention. Such a kitwould preferably comprise HIF-3α antibody(ies) or probe(s) according tothe invention and at least one element selected from the groupconsisting of instructions for using the kit, assay tubes, enzymes,reagents or reaction buffer(s), enzyme(s).

x) Identification of Molecules that Modulate HIF-3α Protein Expression

HIF-3α cDNA may be used to facilitate the identification of moleculesthat increase or decrease HIF-3α expression. In one approach, candidatemolecules are added, in varying concentration, to the culture medium ofcells expressing HIF-3α mRNA. HIF-3α expression is then measured (orexpression of another gene, such as VEGF which expression is regulatedby HIF-3α), for example, by Northern blot analysis using a HIF-3α cDNA,or cDNA or RNA fragment, as a hybridization probe. The level of HIF-3αexpression in the presence of the candidate molecule is compared to thelevel of HIF-3α expression in the absence of the candidate molecule, allother factors (e.g. cell type and culture conditions) being equal.

Compounds that modulate the level of HIF-3α may be purified, orsubstantially purified, or may be one component of a mixture ofcompounds such as an extract or supernatant obtained from cells (Ausubelet al., supra). In an assay of a mixture of compounds, HIF-3α expressionis tested against progressively smaller subsets of the compound pool(e.g., produced by standard purification techniques such as HPLC orFPLC) until a single compound or minimal number of effective compoundsis demonstrated to modulate HIF-3α expression.

Compounds may also be screened for their ability to modulateHIF-3α-biological activity (e.g. VEGF expression, induction ofangiogenesis). In this approach, the biological activity of HIF-3α or ofa cell expressing HIF-3α (e.g. lung or kidney cell) in the presence of acandidate compound is compared to the biological activity in itsabsence, under equivalent conditions. Again, the screen may begin with apool of candidate compounds, from which one or more useful modulatorcompounds are isolated in a step-wise fashion. The HIF-3α or cellbiological activity may be measured by any suitable standard assay.

The effect of candidate molecules on HIF-3α-biological activity may,instead, be measured at the level of translation by using the generalapproach described above with standard protein detection techniques,such as Western blotting or immunoprecipitation with a HIF-3α-specificantibody (for example, the HIF-3α antibody described herein).

Another method for detecting compounds that modulate the activity ofHIF-3α is to screen for compounds that interact physically with a givenHIF-3α polypeptide. Depending on the nature of the compounds to betested, the binding interaction may be measured using methods such asenzyme-linked immunosorbent assays (ELISA), filter binding assays, FRETassays, scintillation proximity assays, microscopic visualization,immunostaining of the cells, in situ hybridization, PCR, etc.

A molecule that promotes an increase in HIF-3α expression or HIF-3αactivity is considered particularly useful to the invention; such amolecule may be used, for example, as a therapeutic to increase cellularlevels of HIF-3α and thereby exploit the ability of HIF-3α polypeptidesto promote and/or induce angiogenesis.

A molecule that decreases HIF-3α activity (e.g., by decreasing HIF-3αgene expression or polypeptide activity) may be used to decrease and/orblock angiogenesis and/or cellular proliferation. This would beadvantageous in the treatment of cancer.

Molecules that are found, by the methods described above, to effectivelymodulate HIF-3α gene expression or polypeptide activity, may be testedfurther in animal models. If they continue to function successfully inan in vivo setting, they may be used as therapeutics to either promotesor inhibit angiogenesis.

xi) Induction of Expression of Angiogenesis-related Gene(s) by HIF-2αand HIF-3α

According to a related aspect, the present invention relates to methodsand cells for inducing angiogenesis and for improving muscular function,and more particularly for treating coronary and cardiac diseases inmammals. The invention also provides genetically modified muscular cellsexpressing a plurality of angiogenesis-related genes.

This aspect of the invention is based on the use of a nucleotidesequence encoding a transcription factor from the hypoxia induciblefactors family (HIF-1α, HIF-2α, and HIF-3α). As it will be shown in theexemplification section, the present inventors have demonstrated thatHIF-2α was stimulating, in addition to VEGF, the expression of othermolecules implicated in angiogenesis such as IL-8, IL-6, PIGF, LIFreceptor, PAI-2 and MMP7 in muscular cells. The inventors showed, in amodel of rat CHF, that HIF-2α could be used for therapeutic angiogenesisin mammals. Also, the inventors have genetically modified skeletalmuscle cells (SkMC) with HIF-2α gene and showed that these cellsdemonstrated superior angiogenic properties in vivo. Furthermore,treatment of CHF rats with HIF-2α gene transfer resulted inangiogenesis, higher metabolic activity and improved cardiac functions.

Since HIF-1α, HIF-2α, and HIF-3α belong to the same family and areclosely related, it is expected that similar results could be obtainedwith any of the HIF members. Therefore, the additional aspects of thepresent invention given in the present section encompasses not only theuse of HIF-2α but HIF-1α and HIF-3α (all isoforms) as well. HIF-1α(GenBank™ accession No. U22431) is described in by Wang et al., (Proc.Natl. Aca. Sci. USA (1995) 92: 5510-5514) and in U.S Pat. Nos.5,882,314; 6,020,462 and 6,124,131. HIF-2α (GenBank™ accession No.U81984) is described by Tian et al., (Genes & Dev. (1996) 11: 72-82),and in U.S. Pat. No. 5,692,963. One isoform of HIF-3α is describedherein and another isoform (GenBank™ accession No. AB054067) has beendescribed by Hara et al. (Biochem. Biophys. Res. Comm. (2001), Oct. 5;287:808-813). All these documents are incorporated herein by reference.

Therefore, this aspect of the invention is directed to a method forinducing in a muscular mammalian cell the expression of at least one,preferably a plurality of angiogenesis-related gene(s), the methodcomprising the step of introducing and expressing in the cell a nucleicacid sequence encoding a functional HIF-2α transcription factor or afunctional HIF-3α transcription factor.

According to another related aspect, the invention is directed to amethod for increasing the metabolic activity of a muscular cell (such asglucose consumption), comprising the step of introducing and expressingin the cell a nucleic acid sequence encoding a functional transcriptionfactor of the Hypoxia Inducible Factor (HIF) family. Preferably, thetranscription factor is HIF-2α or HIF-3α.

In a further related aspect, the invention is directed to a method forimproving cardiac tissue functions of a mammal, comprising the step ofproviding to the cardiac tissue of the mammal a plurality of geneticallymodified cells expressing a nucleic acid sequence encoding a functionalHIF-2α transcription factor or a functional HIF-3α transcription factor.

According to another related aspect, the invention is directed to amethod for inducing angiogenesis in a mammalian muscular tissue,comprising the step of providing the muscular tissue with a plurality ofgenetically modified muscular cells expressing a nucleic acid sequenceencoding a functional HIF-2α transcription factor or a functional HIF-3αtranscription factor.

According to the invention, a nucleotide sequence encoding atranscription factor of hypoxia inducible factor family is introducedand expressed into a muscular cell, preferably a skeletal muscular cellor a cardiac cell by using any suitable method including but not limitedto adenoviral infection, and plasmid, cosmid or artificial chromosometransfection or electroporation. More preferably, the nucleic acidsequence encoding the transcription factor(s) is a cDNA.

In a further aspect, the invention is directed to a genetically modifiedmuscular cell (e.g. skeletal muscle cell, cardiac cell) expressing afunctional HIF-2α transcription factor or a functional HIF-3αtranscription factor. Preferably, the cell is a skeletal muscular cellor a cardiac cell. Preferably also, the cell comprises a cDNA encodingthe transcription factor. As mentioned previously, such cells may beparticularly useful when transplanted in a compatible recipient forinducing angiogenesis, relieving ischemia, increasing the metabolicactivity of a mammalian muscular tissue, and/or increasing muscularfunction in CHF or in peripheral vascular disease, locally or insurrounding transplanted tissue. Of course, the genetically modifiedcells of the present invention could also be used for the formation ofartificial organs or for tissue constructions.

Although transplantation of cells (autologous transplantation or from acompatible donor) is preferred for inducing angiogenesis locally, insurrounding tissue and/or for improving the metabolic activity of amuscular cell and/or for relieving ischemia in coronary heart disease orin peripheral vascular disease and/or for improving the mammal's cardiacfunctions, the nucleic acid sequence encoding the functionaltranscription factor may be introduced directly in the tissue of themammal using any suitable method known in the art (see hereinbefore forsome examples). The angiogenesis-related gene should be expressed at alevel that is sufficient to induce angiogenesis locally or insurrounding tissue.

As it will now be demonstrated by way of an example hereinafter, thepresent invention is useful for inducing angiogenesis, relievingischemia and increasing cell metabolic activity and tissue function inCHD and in PVD.

EXAMPLES

The following examples are illustrative of the wide range ofapplicability of the present invention and is not intended to limit itsscope. Modifications and variations can be made therein withoutdeparting from the spirit and scope of the invention. Although anymethod and material similar or equivalent to those described herein canbe used in the practice for testing of the present invention, thepreferred methods and materials are described.

Example 1 Use of HIF-1α, HIF-2α and HIF-3α for Inducing Angiogenesis andImproving Muscular Functions

Materials and Methods

Plasmids Construction

HIF-1α-VP16/pcDNA3 was obtained from S. L. McKnight (Tian et al., Genes& Dev. (1996) 11:72-82). To generate HIF-1α-VP16/pcDNA3, a VP16 fragment(NheI and blunt ended EcoRI from pVP16 (ClonTech)) was inserted inHIF-1α/pcDNA3 cut with Af/II and XbaI blunt ended in presence of aNheI-Af/II linker composed of the oligos TTA AGA TAT CGA TGA CAC GTG(SEQ ID NO:4) and TCA GCA CGT GTC ATC GAT ATC (SEQ ID NO:5), replacingthe 3′ part of HIF-1α sequence by VP16, putting DNA binding domain andheterodimerization domains (HLH and PAS) of HIF-1α (encoded by the 5′ ofthe gene) in frame with VP16 transcription activation domain.

HIF-2α-VP16/pcDNA3 was obtained from S. L. McKnight (Tian et al., Genes& Dev. (1996) 11:72-82). To generate HIF-2α-VP16/pcDNA3, a HIF-2α 5′region was amplified by PCR using HIF-2α/pcDNA3 as template with theoligonucleotides T7 and GCT AGC TAG GM GTT ACT CCT CTC (SEQ ID NO: 6),creating a NheI at the end of HIF-2α DNA binding domain andheterodimerization domains (HLH-PAS). This fragment was cut with NheIand KpnI and was inserted in place of HIF-1α sequence inHIF-1-VP16/pcDNA3 cut NheI and KpnI. Sequencing confirmed integrity ofthe amplified sequence.

HIF-3α was cloned by RT-PCR by homology deduction from mouse HIF-3αsequence. Using Marathon™ RT-PCR kit (ClonTech), 2 fragments of HIF-3αsequence were amplified from adult human heart RNA (ClonTech) with theoligos CCA TGG ACA GGT CGA CCA CGG AGC TGC GCA AGG (SEQ ID NO:7)(containing an ATG initiator in a NcoI site) and CGC AGG CAG GTG GCT TGTAGG CCC T (SEQ ID NO:8) for the 5′ end and with the oligos CAG CTG GAGCTC ATT GGA CAC AGC ATC (SEQ ID NO:9) and CCC CAT CCT GTG CGT TGG CTGCCG (SEQ ID NO:10) for the 3′ end. Both fragments were sequenced and puttogether with the unique Ndel site, and the reconstructed cDNA wasinserted in the NcoI initiator of HIF-1α/pcDNA3, using HIF-1α Kozaksequence to initiate translation. To generate HIF-3α-VP16/pcDNA3, a PCRfragment containing HIF-3α DNA binding domain and heterodimerizationdomains (HLH and PAS) was amplified using HIF-3α/pcDNA3 as template withthe oligos T7 and GGA GTC AGC TTA AGC TGA ATG GGT CTG C (SEQ ID NO:11).The amplification product was cut with BamHI and Af/II (coming from the3′ oligo) and inserted in place of HIF-1α sequence in HIF-1α-VP16/pcDNA3cut with BamHI and Af/II. Sequencing confirmed integrity of theamplified sequence.

Transfection

Early passage 293 cells (ATCC # CRL-157) were plated at 1,7×10⁶ cellsper plate (100 mm) and grown overnight. 10 μg of sterile plasmid DNA wastransfected with lipofectamin, according to the instructions from themanufacturer. After a 5 hours transfection, cells were incubated eitherin normoxia (5% CO₂ in normal air at 37° C.) or in hypoxia (5% CO₂, 2%O₂ at 37° C.) for 24 hours. ˜70% confluence Hep3B cells (ATCC #HB-8064)in 100 mm dishes were transfected with 4 μg of sterile plasmid DNA with6 μl of Fugene 6™ (Roche), according to the instructions from themanufacturer.

Adenovirus Production

HIF constructs were used to produce adenoviral vectors with the Ad.Easy™technology using manufacturer methodology (Q-Biogene).

Infection

Early passage human SkMC (Cambrex #CC-2561) were plated in 100 mm dishesand grown until they reached ˜70% confluence. Cells were rinsed with PBSand covered with 4 ml DMEM with 10% fetal calf serum (FCS) andadenoviruses at a MOI of 500. This MOI allow infection of only ˜10% ofthe cells. Cells were incubated at 37° C. with constant but gentleagitation for 6 hours. 6 ml of DMEM with 10% FCS was added and cellswere incubated overnight at 37° C. Cells were then incubated either innormoxia (5% CO2 in normal air at 37° C.) or in hypoxia (5% CO2, 2% O2at 37° C.) for 24 hours.

RNAses Protection Assay (RPA)

Total RNA was isolated from transduced cells by Guanidinethiocyanate-phenol extractions as described (Staffa, A., et al., J. BiolChem. (1997) 272: 33394-401) (FIG. 3A or 3C) or with Rneasy Mini Kit™(Qiagen) as described by the manufacturer. 15 μg total RNA per samplewere analyzed by RPA using RPA III kit (Ambion). Probe were preparedfrom hAngio1 template set (Pharmingens) for FIG. 3A or from home madeVEGF and actin template for the others. VEGF template was prepared byamplification on the phVEGF165.SR (from J. F. Isner) (Tsurumi, Y., etal., Circulation. (1996) 94: 3281-3290) with the oligos CCG GM TTC TCTACC TCC ACC ATG CC (SEQ ID NO:12) and CCG GM TTC CTC AGT GGG CAC ACA CTCC (SEQ ID NO:13), digestion of the amplification product with EcoRI (inboth oligos) and insertion in pBluescript cut with EcoRI. Sequenceintegrity was confirmed by sequencing. The resulting plasmid wasdigested with HindIII and transcribed with T7 RNA polymerase to generatean antisense RNA probe. Actin probe template was obtained from W. E.Bradley (Houle, B., et al., Proc. Natl. Aca. Sci. USA (1993) 90:985-989).

Quantification

Autoradiograms were scanned on an Alpha Imager 2000™ (Alpha InnotechCorporation). Intensity of each band was measured and relativeexpression was calculated as VEGF intensity/Flt4 intensity for FIG. 3Aor as VEGF intensity/actin intensity for the others. Relative VEGFvalues were then normalized so that a value of 100 was attributed to thecontrol samples in normoxia. Protein VEGF produced were proportional tothe amount of mRNA quantified. Results are expressed as mean±SED.

Gene Chip Hybridization

Total RNA was isolated from human SkMC (Clonetics) infected with eitherAd.Null™ (Q-Biogene) or Ad.HIF-2α as described (Staffa, et al., J. Biol.Chem. (1997) 272: 33394-401). Probes were prepared and hybridized toAtlas Human 1.2 Array™ (Clontech) with ExpressHyb™ solution (Clontech)according to the instructions from the manufacturer. The arrays wereexposed to phosphorimager screen and analyzed with the Atlas 2.01™software (Clontech).

Angiogenesis in Vivo

Early passage human SkMC (uninfected or infected with the indicatedadenovirus vectors) were incorporated into matrigel (50000 cells/0.5 ml)and injected subcutaneously into skid mice (10 per groups). Matrigelalone or bFGF (400 ng/ml) were used as controls. 7 dayspost-implantation, matrigel plugs were excised and processed forhistological evaluation. Each measurement corresponds to the degree ofcellular response in a microscopic field expressed as Integrated Density(sum of the gray values in the selection, with the backgroundsubtracted, 6 measurements on each plug).

Metabolic activity in infarcted rats created by a permanent leftanterior descending coronary artery ligation (Myoinfarct™ rats, CharlesRiver Laboratories) was measured 5 days post ligature by injection of¹⁸FDG (˜750 μCi/100 g) and dynamic acquisition using a small animalPET-Scan™ (Sherbrooke University). Ten days after the ligature, amini-thoracotomy was performed to inject a solution of Ad.HIF2α/VP16 orsaline (N=2) in the infarcted area of the left ventricle. Another ¹⁸FDGPET-Scan™ was performed 14, 28, 42 and 56 days after the injection.Metabolic activity was calculated as the amount of ¹⁸FDG found in anarea of the lateral wall of the left ventricle, where the infarct islocalized, normalized with the amount of FGD found in an unaffected areain the septal wall that is irrigated by another coronary artery. Afterthe last PET-scan™, animals were sacrificed and blood vessels werequantified in the entire infarcted area or in the fields of the marginsbetween healthy and infarcted tissues.

Results

In Vitro VEGF Induction by HIF-1α, HIF-2α and HIF-3α

FIGS. 2A, 2B, 3A, 3B and 3C illustrate the expression of angiogenesisrelated genes in human cells transfected with HIF constructs.

The natural (wild type) form of HIF factors or activated version wereintroduced in pcDNA3 (Invitrogen Corp.), an expression vector. Activatedconstructs consist in the deletion of hypoxia regulated instabilitydomains located in the N′ part of the proteins and the introduction of astrong activator of transcription, the VP16 domain from Herpes virus(Vincent et al., Circulation (2000) 102: 2255-2261). The resultinghybrids are no longer regulated by hypoxia and always display atransactivation activity.

These plasmids were transiently transfected in human embryonic kidney293 cells (HEK293) or in human liver cells Hep3B. Cells were incubated24 hours either in normoxia (normal conditions) or in hypoxia (2%oxygen) and total RNA was isolated. Similarly, human skeletal musclecells (hSkMC) were transduced with adenovirus vectors expressing some ofthe HIF constructs. Endogenous VEGF gene activation following HIFconstructs transfection was analyzed by RNAse Protection Assay (RPA,Ambion).

No VEGF induction was produced by HIF-1α transfection in normoxia(similar to control) (FIGS. 2A, 2B, 3A and 3B). This result was expectedsince HIF-1α is quickly degraded in normoxia. The HIF-1α/VP16 hybridstimulated VEGF both in normoxia and hypoxia, since the protein is nolonger regulated by oxygen tension. Interestingly, HIF-3α was veryefficient to stimulate VEGF in HEK293 and Hep3B cells (FIGS. 2A and 2B).The levels were superior to those obtained with HIF-1α both in normoxiaand in hypoxia, although HIF-1α/VP16 had an even higher transactivationactivity. The activation of HIF-3α with the VP16 domain did notsignificantly modify the levels of VEGF induction.

VEGF stimulation by HIF-2α was also very important. FIGS. 3A, 3B and 3Cshow that the wild type version of the protein stimulated VEGF in rangescomparable to HIF-1α/VP16, both in normoxia and in hypoxia, in the 3cells types studied (HEK293 in FIG. 3A, Hep3B in FIG. 3B and hSKMC inFIG. 3C). The VP16 fusion did not provide an important advantage in thelevels of VEGF produced.

Activation of Angiogenic Genes by HIF-2α in Vitro

VEGF is an important angiogenic gene. However, angiogenesis is a complexprocess involving several steps that are regulated by several factors.To evaluate HIF factors potential as an angiogenic modulator, geneexpression was compared in human SkMC infected either with Ad.HIF2α orAd.Null™ using gene chip technology. cDNA probes derived from eithercell population was hybridized on a Atlas Human 1.2 Array™ (Clontech)assessing expression of almost 1200 genes. Of the genes differentiallyregulated, VEGF was the one showing the most significant increase. VEGFstimulates both proliferation, migration and differentiation ofendothelial cells. Interestingly, other angiogenic genes were activated(Table 2). As VEGF, Interleukin-8 (IL-8) and the activation of LeukemiaInhibitory Factor Receptor (LIF-R) are known to stimulate theproliferation of endothelial cells. However, IL-8 also acts byactivating the release of metalloproteinases responsible for the basalmembrane disruption, the first step of angiogenesis (FIG. 4). LIF isalso known to enhance survival of SkMC, which would be useful in celltherapy. The role of Interleukin-6 (IL-6) is more indirect: it has noeffect on endothelial cell proliferation, but stimulates their migrationand differentiation. It is also an enhancer of VEGF production.Placental growth factor (PIGF) was shown to act in cooperation with VEGFto stimulate angiogenesis. Matrix metalloproteinase 7 (MMP7) is a potentproteinase able to initiate the angiogenesis process while placentalplasminogen activator inhibitor 2 (PAI-2) is able to stabilize nascentvessels (FIG. 4). There are many other potential angiogenic factors thatcouldn't be detected in this assay because of limitations of the genechip, but that might be induced by HIF factors.

TABLE 2 Genes activated by HIF-2α in SkMC. Gene Fold induction CategoryVEGF 9.10 Growth factor IL-8 2.26 Growth factor IL-6 2.21 Growth factorPIGF Up* Growth factor LIF-R Up* Growth factor PAI-2 1.93 Proteinaseinhibitor MMP7 Up* Metalloproteinase *Inductions labeled “up” arerepresenting the activation from a previously undetected gene.HIF-2α Stimulates Angiogenesis in Vivo

Angiogenic potential of HIF constructs were evaluated in vivo bysubcutaneous implantation of SkMC transfected with HIF constructs inmice. Seven days following implantation, modified cells pellets showedsignificantly higher blood vessel density than unmodified SkMC (FIG.5B). This result confirms that the VP16 activation is not necessary inthe case of HIF-2α. Modified SkMC differentiated in vivo into myotubessupported by extracellular matrix and surrounded by new blood vessels(FIG. 5A). The angiogenesis was important around the myotubes andappeared well organized.

HIF-2α was also directly delivered in a model of MI in rats. Metabolicactivity was assayed 5 days before direct myocardial injection of thevector Ad.HIF-2α/VP16 and at several time points in the following 2months. As shown in FIGS. 6A and 6B, an improved metabolic activity wasmeasured in the infarcted area of treated rats over control ones asquantified by position emission tomography-scan (PET-Scan™). When bloodvessel density was quantified by histology, an increase number of bloodvessels was noted for the adenovirus treated rats in the infarcted area,as well as in the peri-infarcted zone (FIG. 6B).

3) Discussion

In vitro transfection experiments showed that wild type HIF-3α andHIF-2α were superior to HIF-1α to induce VEGF. Used in gene therapy,HIF-3α would thus be very useful to modulate angiogenesis.

As shown in FIGS. 2A, 2B, 3A, 3B and 3C, transfection of HIF-VP16 fusionencoding constructs resulted in a significant stimulation of VEGF.However, in gene therapy in humans, these constructs pose the problem ofimmunogenicity. The presence of the VP16 sequence, of viral origin, isrecognized by the immune system and trigger an immune response againstthe transferred gene. Construct using wild type human genes, such asHIF-3α, has the advantage of being less immunogenic, thus providing alonger period of expression. In comparison, HIF-1α had a poor angiogenicpotential in normoxia and requires the VP16 modification to be fullyactive (FIGS. 2, 3 and Vincent et al., Circulation (2000) 102:2255-2261). FIGS. 2A, 2B, 3A, 3B and 3C also strongly suggest thatHIF-2α and HIF-3α could be used efficiently in gene transfer protocolsto modify gene transcription of the targeted cells. In particular, VEGFexpression is increased, which result in angiogenesis. It is thusproposed to use HIF-2α or HIF-3α sequence in ischemic diseases toincrease blood vessels and blood perfusion.

The analysis of genes activated by HIF-2α revealed the induction ofseveral angiogenic genes (Table I). These genes play a role in variousaspects of angiogenesis (FIG. 4) and the resulting angiogenesis is thusexpected to be strong and well organized. This is a major advantagecompared to the use of solely VEGF to induce angiogenesis since all thekey steps of angiogenesis will be stimulated. It is expected that HIF-3αwill also regulate several angiogenesis related genes, and possibly thesame ones as HIF-2α.

In vivo experiments proved that HIF-2α gene transfer resulted in asignificant angiogenesis, both in sub-cutaneous implants (FIG. 5B) andin a MI heart model (FIG. 6B). These results confirmed that the VP16fusion was not necessary to result in the formation on blood vessels.This characteristic confers an important advantage to HIF-2α sequence asan angiogenic agent. The use of a native sequence in gene transfertherapy will raise a much lower immunogenic response than a constructwith VP16, of viral origin. Since HIF-3α was also superior to HIF-1α andshowed in vitro induction of VEGF similar to HIF-2α, it is expected thatit will also be efficient in vivo.

Angiogenesis resulted in an increase in metabolic activity (increasedglucose consumption) in the infarcted area as shown in FIG. 6A,indicating an improvement in the tissue function. This, higher bloodsupply translated in higher muscle activity which can improve heartpumping function.

In summary, it is clear that HIF factors delivered either directly orvia an implanted cell, offers a great potential for myocardialregeneration and improvement of cardiac function.

The results reported herein constitute a proof of principle to theeffect that HIF-2α and HIF-3α can be used in gene therapy.

While several embodiments of the invention have been described, it willbe understood that the present invention is capable of furthermodifications, and this application is intended to cover any variations,uses, or adaptations of the invention, following in general theprinciples of the invention and including such departures from thepresent disclosure as to come within knowledge or customary practice inthe art to which the invention pertains, and as may be applied to theessential features hereinbefore set forth and falling within the scopeof the invention or the limits of the appended claims.

1. An isolated or purified nucleic acid comprising a nucleotide sequenceselected from the group consisting of: the nucleotide sequence of SEQ IDNO: 1; the nucleotide sequence that is fully complementary to thenucleotide sequence of SEQ ID NO: 1; and nucleotide sequences having atleast 95% identity to the full length of the nucleotide sequence of SEQID NO:
 1. 2. The nucleic acid of claim 1, wherein it comprises anucleotide sequence having at least 95% nucleotide sequence identity tothe full length of a nucleic acid encoding the amino acid sequence ofSEQ ID NO:
 2. 3. The nucleic acid of claim 1, wherein it encodes apolypeptide having the biological activity of a human Hypoxia InducibleFactor-3 (HIF-3) polypeptide.
 4. The nucleic acid of claim 1, whereinsaid nucleic acid consists of a cDNA.
 5. A cloning or expression vectorcomprising the nucleic acid of claim
 1. 6. The vector of claim 5,wherein said vector is capable of directing expression of a peptideencoded by said nucleic acid in a vector-containing cell.
 7. The vectorof claim 5, wherein said vector is selected from the group consisting ofplasmids, cosmids, artificial chromosomes, adenoviruses,adeno-associated viruses, retroviruses, herpes simplex viruses,alphaviruses, and lentiviruses.
 8. A transduced cell that contains thenucleic acid of claim
 1. 9. The cell of claim 8, wherein said cellconsists of a cell selected from the group consisting of HEK293 cells,Hep3B cells, mammalian skeletal muscular cells, cardiac cells, bonemarrow cells, fibroblasts, smooth muscle cells, endothelial cells,endothelial progenitor cells and embryonic stem cells.